Difference between this and unpermitted RMT would be : where the money goes. SE would get the money from those token purchases, not some RMT company that puts bots at main city Aetherytes and boards to say some gil advertisement every few seconds. Effectively, those tokens allow someone (John) to pay someone else (Arthur) Gil, in exchange for Arthur providing John with game time purchased from SE.
Is it RMT? Yes; but RMT from SE happens every time someone buys any in game Glamour or Phantasia from the Mogstation.
As for allowing botting .. no. Non-RMT botting should be banned just as fast as RMT botting.
